BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ

GigaScience

Olivier Collin²  Fabrice Legeai¹  Yvan Le Bras²  Cyril Monjeaud²  Anthony Bretaudeau² 

[1] INRIA, IRISA, GenScale, Campus de Beaulieu, Rennes 35042, France;INRIA, IRISA, GenOuest Core Facility, Campus de Beaulieu, Rennes 35042, France

关键词: Data libraries;    Data manager;    Reference data;    Galaxy;    BioMAJ;   

Others  :  1204329
DOI  :  10.1186/s13742-015-0063-8

 received in 2014-12-22, accepted in 2015-04-22,  发布年份 2015

【 摘 要 】

Background

Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit).

BioMAJ is a widely used and stable software that is designed to automate the download and transformation of data from various sources. This data can be used directly from the command line, in more complex systems, such as Mobyle, or by using a REST API.

Findings

To ease the process of giving access to reference data in Galaxy, we have developed the BioMAJ2Galaxy module, which enables the gap between BioMAJ and Galaxy to be bridged. With this module, it is now possible to configure BioMAJ to automatically download some reference data, to then convert and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

Conclusions

The developments presented in this paper allow us to integrate the reference data in Galaxy in an automatic, reliable, and diskspace-saving way. The code is freely available on the GenOuest GitHub account (https://github.com/genouest/biomaj2galaxy webcite).

【 授权许可】

   
2015 Bretaudeau et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

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